IGB Developer's Guide
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Version Control

The Genoviz project uses Subversion for version control and managing the release cycle. The repository is hosted at sourceforge.net.

Anyone contemplating contributing to the Genoviz code base should read this on-line text on Subversion before getting started: Version Control with Subversion.

Note that for many years, Genoviz used CVS for version control. We migrated from CVS to subversion in 2008.

 

IGB code base

IGB uses several libraries and sub-projects within the genoviz repository, including 

  • genometryImpl - data models shared by DAS server code and IGB
  • genoviz_sdk - graphics library that implements zooming, interacting with views, etc.
  • igb - the core IGB application
  • plugins - IGB tabbed panels
  • common - ?

Structure of the repository - trunk and branches

The repository contains branches and a main trunk of development.

Branches

There are two types of branches - release branches and feature branches.

Release branches have names like "igb_6_4" and correspond to major releases of the software we have made for end users. These should never be removed from the repository and should not ever be touched except by the group managing releases for end users. (As of this writing, this is the team at UNC Charlotte led by Ann Loraine. If you have any questions about this, contact her.) 

Feature branches are development workspaces and may ultimately be merged backed into the trunk provided they pass testing. If you have a great new idea for an IGB feature or a change the the user interface, first make a branch and implement your changes there. If you are interested in working on the GenoPub code, contact David Nix.

Do not develop on the trunk unless your proposed new feature is bug fix or is highly unlikely to introduce new bugs to existing systems and features. If you have any questions about this, please contact the IGB development team directly or via the developers' list.

Why branch for new features?  

There are two major reasons you should implement new features on a feature branch rather than the trunk:

  • IGB is a mature software application with thousands of users and hundreds of features. New developers experience a steep learning curve as they master the code base. Developers new to molecular biology, genomics, or next-generation sequencing often have an even steeper learning curve as they get familiar with IGB basic functionality. If you are new to the IGB and Genoviz code base, you will need freedom to experiment and make mistakes without annoying other developers or disrupting the release cycle. Creating a branch gives you a risk-free workspace where you can work, experiment, and back out of changes as needed. However, this doesn't mean you'll be developing in isolation - you can always merge in changes from the trunk. Before you get started, read this: Chapter 4: Branching and Merging in Version Control with Subversion.
  • IGB is a graphical user interface and therefore requires extensive manual testing every time a change is made either to the user interface or the underlying code base. Before merging a branch back into the trunk, you must demonstrate that the new feature is well-tested and bug-free. The Loraine group at UNC Charlotte has a testing team that can help you, but please be aware that resources are limited. If your new feature requires extensive testing and is not already covered in one of the group's funded grants, you will need to contribute to the testing effort. Contact Ann Loraine for more details.

The main trunk of development should not be used to "try things out" or experiment with new ideas and architectures. If you want to try something new that is likely to cause many other features to break or that you are not sure will work, then first make a branch and develop it there.

Table of Contents

IGB git repo (main)

The main repository address is: https://bitbucket.org/lorainelab/integrated-genome-browser.

The IGB project uses git for source code management. We use maven and Bitbucket pipelines to build and release IGB artifacts and user-friendly installers. 

Genoviz SDK

IGB depends on the Genoviz Software Development Kit (Genoviz SDK) which is version-controlled in a separate repository at https://bitbucket.org/lorainelab/genoviz-sdk. When you build IGB, the compilation tool we use (mvn) will obtain the latest copy of the genoviz compiled code (a "jar" file) and install it locally.

Maven 

The IGB project uses maven to build IGB, IGB Apps, and the GenoViz SDK. We provide access to new and old IGB-related jar files using the following maven repositories:

To include these in your project, see the top-level POM.xml file in the Integrated Genome Browser project code base.

History

The original GenoViz library - called "BioViews" - was first developed by Gregg Helt at UC Berkeley as part of his PhD research in the mid-1990s. Around then, Helt and two colleagues (Martin Reese and Cyrus Harmon) formed a bioinformatics software company called Neomorphic, which licensed the software from the University. With funding and development support from the Bioinformatics Department at Smith Kline Beecham, they continued to improve the library, renaming it the Neomorphic Genome Software Development Kit. Also during this period, Celera Genomics and the Institute for Genomic Research (TIGR) hired Neomorphic to build genome browser and annotation software. Ann Loraine joined the company in 1999 and helped build the Neomorphic Annotation Station for The Institute for Genomic Research. 

In October 2000, Affymetrix purchased Neomorphic and re-focused software effort on supporting and developing Affymetrix DNA microarray products. In 2001, Gregg Helt and colleagues began developing Integrated Genome Browser to visualize and analyze data from genome tiling arrays, which contained probes selected from (mostly) regular intervals along the genome. Visualization of probe intensity data alongside gene models was essential to developing algorithms to normalize and analyze the data, and the team at Affymetrix developed some of the first visual analytics algorithms in bioinformatics. Also, they developed some of the first indexed, random access file formats to enable partial loading of data sets that were too large to fit into computer memory. Support from Affymetrix along with federal grants to PIs Tom Gingeras and Gregg Helt funded early IGB development during this period. Affymetrix released IGB as part of their NetAffx Web site in the early 2000s.

In 2004, Affymetrix released IGB and NGSDK as open source software. This first release was done as a "tarball" on their Web site. In Jan. 2005, Affymetrix developers imported the tarball contents into a new CVS repository at Sourceforge and began using that for further development, discarding the internal repository at Affymetrix. In addition, they changed the name of the graphics library from "Neomorphic Genome Software Development Kit" to "Genoviz Software Development Kit". However, many of the graphics library's class names retain the prefix "Neo" - e.g., NeoWidget, NeoMap, etc.

In 2004, Ann Loraine joined the University of Alabama at Birmingham as an Assistant Professor, where she wrote funding proposals requesting further support for IGB and the Genoviz SDK. In 2008, she joined the College of Computing and Informatics at UNC Charlotte. Later that year, NSF awarded her a new grant to develop IGB and its companion data distribution site IGB Quickload. Developers at Affymetrix continued contributing to the code for several years after that. You can see their work by searching for commits from developers "chyekk" (Ed Erwin) and "gregghelt." 

After joining UNC Charlotte, Loraine and colleagues migrated the code to a subversion repository, also hosted at Sourceforge.  We continued to use this repository for many years. In 2014, we migrated the source code for IGB and the Genoviz SDK to a new git repository hosted at Atlassian's Bitbucket. 

Unfortunately, over the years the early development history pre-dating the 2004 open source release has been lost. In addition, early products built using Genoviz SDK are also lost. When the developers at Affymetrix prepared the first open source release, it seemed simpler and less risky to simply migrate the code directly into a new CVS repository and go from there. Now, of course, we are using tools that are more sophisticated than before, and we can easily trace how the code has changed dating from Jan 2005 until the present day.  If you have questions about what you see, feel free to get in touch.

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